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parallelSlotNames() was renamed vertical_slot_names() in S4Vectors 0.25.14

Hervé Pagès authored on 24/03/2020 06:15:16
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@@ -1,5 +1,5 @@
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 Package: bsseq
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-Version: 1.23.0
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+Version: 1.23.1
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 Encoding: UTF-8
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 Title: Analyze, manage and store bisulfite sequencing data
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 Description: A collection of tools for analyzing and visualizing bisulfite
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@@ -11,10 +11,10 @@ Depends:
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     R (>= 3.5),
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     methods,
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     BiocGenerics,
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-    GenomicRanges (>= 1.29.14),
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-    SummarizedExperiment (>= 1.9.18)
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+    GenomicRanges (>= 1.33.6),
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+    SummarizedExperiment (>= 1.17.4)
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 Imports:
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-    IRanges (>= 2.11.16),
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+    IRanges (>= 2.21.6),
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     GenomeInfoDb,
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     scales,
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     stats,
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@@ -23,7 +23,7 @@ Imports:
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     locfit,
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     gtools,
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     data.table (>= 1.11.8),
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-    S4Vectors (>= 0.23.11),
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+    S4Vectors (>= 0.25.14),
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     R.utils (>= 2.0.0),
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     DelayedMatrixStats (>= 1.5.2),
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     permute,
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@@ -22,10 +22,12 @@
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 # Internal methods -------------------------------------------------------------
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-# NOTE: Combine the new parallel slots with those of the parent class. Make
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-#       sure to put the new parallel slots *first*.
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+# NOTE: Combine the new "vertical slots" with those of the parent class. Make
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+#       sure to put the new vertical slots **first**. See R/bindROWS.R file in
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+#       the S4Vectors package for what slots should or should not be considered
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+#       "vertical".
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 setMethod(
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-    "parallelSlotNames",
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+    "vertical_slot_names",
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     "FWGRanges",
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     function(x) {
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         c(GenomicRanges:::extraColumnSlotNames(x), "seqnames", "ranges",
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@@ -35,7 +35,7 @@ setValidity2("FWIRanges", .valid.FWIRanges)
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 # Internal methods -------------------------------------------------------------
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-setMethod("parallelSlotNames", "FWIRanges",
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+setMethod("vertical_slot_names", "FWIRanges",
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           function(x) c("start", "NAMES", callNextMethod())
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 )
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@@ -53,7 +53,7 @@ setMethod("end", "FWIRanges", function(x) {
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 setMethod("names", "FWIRanges", function(x) x@NAMES)
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-setMethod("parallelSlotNames", "FWIRanges",
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+setMethod("vertical_slot_names", "FWIRanges",
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           function(x) c("start", "NAMES", callNextMethod())
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 )
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